score_nlst: Compute the number of LSTs, normalized by the number of WGD...

In yannchristinat/oncoscanR: Secondary analyses of CNV data (HRD and more)

Compute the number of LSTs, normalized by the number of WGD events.

Description

Compute the number of LSTs, normalized by the number of WGD events.

Usage

score_nlst(segments, n.wgd, kit.coverage, threshold = 15)

Arguments

segments	A GRanges object containing the segments, their copy number and copy number types.
n.wgd	Number of whole-genome doubling events (0 if diploid).
kit.coverage	A GRanges object containing the regions covered on each chromosome arm.
threshold	A number above which the test is returned positive (>=).

Details

Compute the number of LSTs in non-LOH segments via the score_lst function and subtract the extra noise induced by WGD events: nLST = LST - 7*W/2 where W is the number of WGD events. A sample is HRD positive (deficient in HR pathway) if nLST is greater or equal to the threshold (15 by default). This score was linked to BRCA1/2-deficient tumors.

Value

A named list with the number of nLSTs and the corresponding label ('Positive', 'Negative').

Examples

w <- score_estwgd(segs.chas_example, oncoscan_na33.cov)
score_nlst(segs.chas_example, w['WGD'], oncoscan_na33.cov)

yannchristinat/oncoscanR documentation built on Oct. 27, 2023, 11:19 p.m.